I'm of the opinion that the Ballista's Shouldn't target the player's.
Alternatively, there could be an adjustable setting on the Ballista's themselves.

As an example: The options could be Target Enemy (Mobs with Red HP Bars.) and
Target All (this setting could be for Mob Farms and/or PVP situations.)
The default setting when the Ballista is placed, I feel should be Target Enemy

Additionally, if possible, the person who places the Ballista should never be considered a target of that Ballista.

The Ballista's are magical self-targeting structures and the Black Metal Traps along with the Wooden Spikes are indiscriminate defense structures that don't do any sort of targeting whatsoever, they are meant to be run into by the enemy.
If you as the player do that, that's on you as the player when it comes to indiscriminate structures.
The Ballista's in my opinion should be set up differently as they are a more advanced kind of defensive structure.